Closed caufieldjh closed 1 year ago
During the most recent Jenkins build, this happens while producing the nt version of the merged graph:
18:17:18 [KGX][cli_utils.py][ merge] INFO: Merged graph has 555871 nodes and 4425365 edges 18:19:24 [KGX][cli_utils.py][ merge] INFO: Writing merged graph to merged-kg-tsv 19:02:00 [KGX][cli_utils.py][ merge] INFO: Writing merged graph to merged-kg-nt 19:22:06 Traceback (most recent call last): 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/run.py", line 167, in <module> 19:22:06 cli() 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__ 19:22:06 return self.main(*args, **kwargs) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1055, in main 19:22:06 rv = self.invoke(ctx) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke 19:22:06 return _process_result(sub_ctx.command.invoke(sub_ctx)) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke 19:22:06 return ctx.invoke(self.callback, **ctx.params) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke 19:22:06 return __callback(*args, **kwargs) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/run.py", line 86, in merge 19:22:06 load_and_merge(yaml, processes) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/kg_idg/merge_utils/merge_kg.py", line 34, in load_and_merge 19:22:06 merged_graph = merge(yaml_file, processes=processes) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/kgx/cli/cli_utils.py", line 728, in merge 19:22:06 transformer.transform(input_args, output_args) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/kgx/transformer.py", line 281, in transform 19:22:06 sink = self.get_sink(**output_args) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/kgx/transformer.py", line 436, in get_sink 19:22:06 return s(self, **kwargs) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/kgx/sink/rdf_sink.py", line 75, in __init__ 19:22:06 self.property_types = get_biolink_property_types() 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/kgx/utils/kgx_utils.py", line 487, in get_biolink_property_types 19:22:06 property_type = get_type_for_property(p) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/kgx/utils/kgx_utils.py", line 529, in get_type_for_property 19:22:06 t = get_type_for_property(r) 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/kgx/utils/kgx_utils.py", line 522, in get_type_for_property 19:22:06 r = e.range 19:22:06 File "/var/lib/jenkins/workspace/nowledge-graph-hub_kg-idg_master/gitrepo/venv/lib/python3.9/site-packages/jsonasobj2/_jsonobj.py", line 160, in __getattr__ 19:22:06 return super().__getattribute__(item) 19:22:06 AttributeError: 'EnumDefinition' object has no attribute 'range'
KGX tries to get the range of something without it.
Workaround: don't produce the nt version. It's really preferable to have it, but for now it is breaking the build.
Describe the bug
During the most recent Jenkins build, this happens while producing the nt version of the merged graph:
KGX tries to get the range of something without it.
Workaround: don't produce the nt version. It's really preferable to have it, but for now it is breaking the build.